In the Eyes of Justice
by Nightfire237
Summary: Naruto Uchiha, direct descendent of Madara, has finally accomplished his goal. With the loss of the Kyuubi, and those dear to him, Naruto barely clings to sanity as he is transported to a world of heroes. There, he joins the Justice League, and becomes the overseer of the newly formed Young Justice. Naruto must master his Mangekyo Sharingan and fight all who threatened the peace...


**Disclaimer: I do not own Naruto or Young Justice**

**"Creature Talking"**

"Character Talking"

_'Character Thoughts'_

**Hello Readers, and welcome to my Fourth Story! I was planning to go with the Bleach/ Young Justice Crossover, and I'll still write it, don't worry. I really had an urge to write a Naruto story where Naruto has the Mangekyo Sharingan as you probably noticed in my profile. Note that Naruto will not use it all the time, and in fact, he'll barely use it at all. Also, there are a few major differences between my Naruto and anime Naruto. My Naruto DID have the Nine-Tails sealed in him, but it was forcibly extracted when he was captured by a COMBO of Nagato and Konan, only to be revived by Nagato later on. Since he no longer carries the Nine-Tails, his dormant Uchiha blood awakens, (he's the descendent of Madara), and he gains the Sharingan Eyes. Consider this a warning to anyone who doesn't like non-canon Naruto.  
**

**I you don't like the idea of Naruto as an Uchiha, then don't read!**

**Anyways, afterwards, he witnesses Kakashi die from Deidara's explosion, which incinerates his body, along with his eye. Later, he defeats and kills Obito, but is unable to get to his eye before Madara destroys his body. Now, we arrive at the present time, where Naruto is in his last moments of life as he faces his grandfather for the final time. Happy Reading Everyone!**

* * *

**Chapter 1: The Last Uchiha**

Naruto gasped heavily as he glared at Madara through his bleeding crimson eye. Madara didn't acknowledged his anger as he cupped his hand to his eyes, staining it with blood. They both knew that one thing couldn't be denied. They had both overused their Mangekyo Sharingan, however, Naruto's eye's were not at their peak yet. The only reason he was still alive was simple. He was the better Shinobi.

The claim be stronger than Madara Uchiha seemed to be far-fetched, and somewhat arrogant, but both knew it was true. Naruto was a true prodigy, and a true genius, despite his fifteen years of age. He had been trained by all three of the Sannin, including Orochimaru, who had tried to forge him into a weapon, ruining his innocence in the process. Naruto chose to summon snakes instead of Toads, claiming he wanted to forge his own legend.

While Madara carried more power with his Wood Release, as well as the Rinnegan, Naruto had something else. While he didn't carry the power of a Tailed Beast, his Susanoo carried the power of the Ten-Tails in it's weaponry. The only reason Naruto was still alive was due to this fact. However, he knew that he didn't carry the Eternal Mangekyo Sharingan. If he didn't end this soon, he would die.

He had traveled too far and fought too hard to get to where he was now. Too many had sacrificed themselves to save his. Kakashi, who was killed by a reanimated Deidara...

Shino, Hinata, and Neji, who had been killed shielding him from Madara...

Sasuke, and Sakura, who had perished at the hands of Obito...

Shikimaru, and Temari...

Jiraiya...

Tsunade...

Nagato...

Konan...

There were so many who had died for him, and he didn't deny that it changed him greatly. It was said that when an Uchiha lost those precious to them, it destroyed their mind, and they would lose themselves within their own hate in the process, but Naruto wasn't like other Uchiha. He held on to his sanity, and when the final time came, he unleashed his venomous hate. He let loose all the rage and power he was hiding at full strength, and was able to go toe-toe toe with Madara, despite Madara's possession of the Rinnegan and the Wood Release.

He knew he wasn't much more of a saint than his own Grandfather. His hands were stained with the blood of innocents as much as his family, and he had done many things he regretted. He had been playing the villain for too long, and he was tired of hiding in the Shadows. Now, he was going to put everything on the line... and finally step into the Light...

* * *

**In the City of Metropolis...**

Naruto opened both his eyes as he stared blankly at the beautiful city lights below. His arms were crossed over his chest as he leaned against the rooftop of a high tower, his long coat swaying in the wind. There was almost nothing to do here anymore. In fact, when he first arrived to this new world, he was somewhat excited. But now, he felt nothing but emptiness. His existence was empty, and he no longer felt a reason to live any longer.

He missed Konoha, and he felt lonely without the Kyuubi speaking to him. He had gotten rather used the Tailed Beast at the end. Besides, it wasn't like he could enter his mindscape and talk to his Susanoo. The very thought was ludicrous. He allowed himself to smile balefully as he sighed, and looked up at the dark night sky. While Kyuubi was a living powerful mass of chakra, Susanoo was merely a weapon of destruction, nothing more. It wasn't the same without Kyuubi around...

Not a single star twinkled in the heavens above. Naruto's dark blue eyes closed gently in accepting disappointment.

His life began with the Sealing of the Nine-Tails, but from them on things changed. Naruto was stolen from his home. And on that day, Naruto's entire life too a drastic turn. His dream to be Hokage was nonexistent. Orochimaru raised him to hate Konoha and those in it, until the day he met Jiraiya, who told him the truth about his origins. Naruto didn't believe it at first, but Orochimaru confirmed his suspicions when he tried to steal Naruto's body in his own greed and lust for power.

Barely escaping, and barely alive, Naruto wandered throughout the Elemental Nations, until he met someone he though he would never meet in his wildest dreams. And, at the tender age of seven, he was adopted... by Tsuande of the Sannin. Together they evaded the Akatsuki, and finally returned to seek refuge in Konoha.

Life there wasn't as easy as Naruto would have liked. He was ostracized, and labeled as a Demon. The Villagers shunned him, and he was nearly harmed many times, but he was too strong to be pushed around by them. They feared that he carried the stench of Orochimaru on him, and they envied that Tsuande had taken pity on him, but Naruto didn't want their acceptance. He only wanted one thing. To protect what Tsuande wanted to protect, even if no one knew that it was him.

So, he trained with Jiraiya and Tsuande, and when he was twelve, the Akatsuki finally began their attack. Naruto fought for the lives of his fellow jinchuuriki as he had managed to kill Hidan and Sasori with much difficulty. However, it wasn't enough. When Pain and Konan attacked the Leaf just to get to him, he didn't stand a chance. He was captured, and his Tailed Beast was sealed. That was Naruto's first time experiencing loss.

As he lay dying, his only family, Tsuande gave up her life to save his, killing herself in the process. And when Naruto realized what he had done... he turned on the Village. Only Jiraiya knew his true intentions as he protected the Leaf from the shadows, as a true Shinobi...

Not too far away, flying high in the sky, a muscular man in red and blue hovered in the night sky, pausing to examine the high towers ahead. An 'S' was on engraved on his chest, and his crimson cape flowed in the high winds. He flew towards one of the towers, and landed gently on it. He was here for only one reason, and one reason alone.

'"Where is he," he muttered as he used his x ray vision. "Why must he always pop out of the shadows when I'm not expecting it?"

"What is it you want from me," a voice said from behind him. Superman whipped around to see a man leaning against a post. He stood at about 5'10''. His blonde hair with small black streaks hung over his forehead and ran down to his shoulders, partly in a ponytail. A black and blue camouflage face mask covered his mouth and nose. A long black trench coat hung down to his lower knees, and two long knives were strapped to his back in an 'x'. His glowing deformed eyes blazed red in the darkness as he glared at Superman fiercely.

Superman's gaze hardened slightly as he stared down the younger man, like a father scolding a son. Naruto narrowed his eyes at the hero, not batting a single eyelash.

"Well, what's the matter?" Naruto asked calmly. His crimson eyes didn't reveal a single emotion.

Superman balled his fists as he fought to keep calm. "I have to talk to you," he said tightly. He knew that Naruto had earned his and the others respect long ago, but he still hadn't earned their trust.

Naruto raised an eyebrow, seemingly unconcerned as he turned away from Superman. "We have nothing to talk about," he said shortly as he walked to the edge of the building. Superman gritted his teeth in anger. Naruto made ready to leap off, but suddenly, another arm clenched hard on his shoulder.

Naruto looked behind him in mild surprise as Superman gripped his shoulder so hard, it creaked under the pressure. Naruto didn't even filch as Superman applied more pressure, his eyes flashing in anger.

"What was that today? What were you thinking," he demanded furiously. Naruto didn't answer as stared back at Superman emotionlessly.

"If you are concerned with my actions today, think nothing of it," he said finally, slipping himself out of Superman's grasp. "I merely was diong what had to be done. As I recall you got in my way, Superman."

"Doing what had to be done!" Superman said incredulously. "You nearly killed Wotan! And you would've succeeded, if we hadn't intervened. You tortured him until he couldn't withstand the pain!"

"And for good reason," Naruto answered back calmly. "He was about to kill innocent civilians, and I did what was necessary to ensure their survival. If you aren't willing to make the same sacrifice, that's your issue, not mine." He began to walk away.

"You're not going anywhere," Superman growled as he reached out to grab Naruto.

Naruto grabbed the hand easily as his eyes blazed red. "I don't have to explain myself to you," he said expressionlessly. Superman snarled, but Naruto stared back, unflinching.

Naruto was about to take some action, but suddenly, he felt a vibration on his belt. His eyes snapped up to meet Superman's as both pushed their belt buckles and felt themselves whisked into the air by a zeta tube. An emergency summon had interrupted their conversation, but Naruto knew that Superman wasn't done lecturing him out yet. And neither was Batman.

* * *

**At the Ruins of Cadmus...**

Superboy and the other stared at the luminous full moon in the sky. Superboy stared longingly in wonder as he finally gazed on the full moon for the first time. The pale white shined on the team as they gave each other triumphed grins. They had done it!

Suddenly, without warning, a figure appeared out the center of the brightness of the moon, like a god ascending from heaven. A cape flowed behind the figures back.

"Superman," Superboy breathed as Superman landed on the ground, followed by other Leaguers.

Robin looked around anxiously as they were surrounded by an airborne Martian Manhunter, Zatarra, and others.

"The entire league is here," Kid Flash gulped as his he looked around in a circle, like a animal trying to escape. Aqualad narrowed his eyes as he spotted someone else, right behind Superman.

Naruto stood on the back of a large raven directly behind Superman as he gazed emotionlessly at the young group of sidekicks and the destroyed building of Cadmus. His arms were crossed as his killer intent pierced the air itself lightly, making all who surrounded him shiver in fear.

"Do you guys feel that," Kid Flash whispered in fright. It felt like something was choking him to death, slowly crushing the life out of him.

Superboy's eyes darted around as he searched for the source while Aqualad and Robin froze in fear, sweat dripping down their faces. Superman's neck tingled as the hair on his arms stood on end. Naruto sighed and rolled his eyes as his killer intent dissipated slowly, disappearing into the air.

Superman shook his head as he looked back the young heroes.

Superboy stepped forward hesitantly. It wasn't easy to read his emotions, but anyone with training could tell he was nervous. Naruto looked on in curiosity as Superboy gently peeled up his tattered white shirt to reveal... an 'S' symbol. The symbol for Superman.

Superman's expression darkened as the other League Members looked at each other in wonder and curiosity. Superboy smiled at Superman, but he was only met with cold dismissal.

Naruto raised an eyebrow as Superboy frowned and met Superman's gaze defiantly. "I'm Superman's clone," he said coldly, finally breaking the tense silence.

Whispers floated throughout the place as Naruto looked at Superboy with something akin to interest.

'_So, they managed to create a clone of the most powerful hero on the planet so easily. Interesting,'_ he mused.

Superboy felt as though he was being watched. He looked at man standing slightly behind Superman, and his eyes narrowed, almost like he was challenging him. If Naruto was any younger, he would've smirked cockily, demanding a fight, but things were different now. Naruto remained silent as he observed Superboy his piercing sharingan, the three tomoe in his eye spinning slowly.

His eyes widened slightly as witnessed a significant increase in power after Superman turned him away. He almost smiled in understanding. It seemed that Superboy, like the Uchiha Clan... grew in power based on his own anger. However, Naruto knew the dangers of hate and revenge. If Superboy continued the way he was, he would undoubtedly fall to the darkness like so many others had.

Naruto watched, seemingly uninterested as some of the Leaguers transported the body of a massive grey monster. Apparently, the sidekicks had managed to defeat it. He watched as Batman and Flash stood before the boys. Naruto vanished into the shadows as he materialized up next to them to listen to the conversation.

Batman stood before the heroes, his furious gaze resting upon each of them in turn. Unlike before, they stared back defiantly. They knew they had disobeyed direct orders, but they were prepared to deal with the consequences, and they didn't regret their actions one bit.

"Cadmus will be investigated," Batman assured them somberly. "But let's make one thing clear-"

"You should've called," Flash interrupted indignantly. Batman shot him a 'shut up or I'll make you look.'

"End results aside, we are not happy," Batman growled, his mouth set in a firm line. The team looked at each other as Batman continued to inform of their disrespect and lack of protocol. Robin's mouth was slightly upturned as he watched Batman ramble on, seemingly enjoying himself.

"-You won't be doing this any longer," Batman said firmly.

They all looked at each other before Aqualad stepped forward. "I am sorry-," he apologized beforehand. "-But we will."

"Aqualad, stand down," Aquaman commanded sternly.

"Apologies my king," Aqualad said, bowing slightly. "But no."

Aquaman's raised an eyebrow in surprise as Aqualad was joined buy the rest, who stood beside him. "We did good work here tonight. The work you trained us to do. Together, on our own, we forged something powerful. Important!"

"Batman, we're ready to use what you taught us," Robin exclaimed softly. "Or why teach us at all?"

The Justice League member close by had thoughtful expression on their faces, considering hard about what had been said.

"Why let them tell us what to do," Superboy demanded angrily. He walked forward to stand beside the rt of the team, as if directly issuing a challenge to the Justice League. "It's simple," he snarled. "Get on board, or get out of the way!"

Batman's eyes narrowed until they were reduced to pearly white slits. It seemed as though he was angry, but in reality, he was deeply pondering on what action to take next with the newly formed, elite Young Justice.

Naruto closed his eyes, and when they snapped back open, his sharingan had disappeared. He made a single handsign, and vanished into a swirl of leaves. He knew now what was going on. The Justice League was finally growing a few brain cells.

* * *

**At Mount Justice...**

Robin, Kid Flash, Aqualad, and Superboy stared at the cave in wonder, their mouths slightly agape. It was certainly a magnificent sight to behold. The ceiling was so high, they couldn't even see it, and the air was cool and refreshing. While Mount Justice was highly rugged and well hidden from prying eyes, it maintained its well-hidden high tech.

Screens rapidly opened in midair, as Batman walked back and forth before the sidekicks. His usual scowl was present on his face as his cape billowed out behind him, but something was different about today. He seemed even more tense and angry than usual. Robin stared at his mentor worriedly. He wondered exactly what was going on. They had been here for nearly twenty minutes. Batman had already told them what was going to be done, and he was just informing them about their instructors, but he had froze halfway.

'_I can't do it,'_ he thought to himself, gritting his teeth. '_I can't go through with this plan. Even if he's the best suited for the job, I just can't do it! This is completely ridiculous!'_

He breathed out slowly, trying to calm his nerves. There was no fighting it now. The vote wasn't unanimous, but it was closer than any others had been for only one reason. This person would relate to the kids the most. He was closest to their age, could protect them all if need be... and was the best at maintaining absolute secrecy. In other words, he was the best working in the Shadows. And that was what the team needed.

For a special ops covert team that operated in the shadow of the Justice League, it's leader had to be someone who was a master of operating in the shadows, and there was only one obvious choice.

Batman turned to face the team again, with a heavy heart. He knew he was going to have to swallow his personal feelings for now and work with it. As much as Batman detested it, this person was the best choice to supervise Young Justice.

"As I was saying before," he said sharply. "The Five of you will be that team."

"Cool!" Robin exclaimed. "Wait, five?" he asked, suddenly feeling confused.

"Yes," Batman said shortly as the Martian Manhunter stepped out of the shows along with a smiling cheerful redheaded girl with similar emerald skin.

"This is the Martian Manhunter's niece, Miss Martian," Batman said in introduction.

"Hi," she chirped happily, waving excitedly at the rest of the team. Kid Flash and the others crowded around her, welcoming her warmly. Even Superboy managed a small smile. Her smile was contagious. Batman inwardly cringed as he prepared himself.

"This will be your Head Supervisor," he droned, motioning behind him. The team sported various expressions at this revelation. Robin looked peeved. Superboy looked angry. Aqualad looked curious. Kid Flash seemed exasperated, and Miss Martian looked curious.

Suddenly, someone materialized from the shadows in a swirl of fire. Aqualad's eyes widened as he recalled the man from the other day.

"This is Deathshadow," Batman said icily. "And he will be in charge from now on."

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**Author's Note: Well, that's all for now. Please tell me what you think via reviews and messages. How can I make this story better? Please let me know. Also, if anyone is interested in Beta-Reading any of my stories, please let me know. It would be much appreciated. Thanks!**

**Next Up: Naruto's previous conversation with Batman is revealed, and Naruto's first real test for the team begins...**

**PS: If some don't like the name I chose for Naruto, sorry about that. Please review or message me any suggestions you might have on better ones. Also, I'll be posting another story with Ulquiorra as the main character, so keep a lookout. Various Naruto characters can be voted to be put in this story via poll!  
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